NN-588 Frontend bugfix & new Stuff

-added sizeable verticalpane
-fixed filter unwillingly closing
-added auto hiding labels
-fixed filter not correctly resetting on graph switch
-fixed overlapping node pane statistics
-fixed correct subset/term/citation switch to other view

frontend/src/components/PersistentWindow.vue

@@ -28,13 +28,12 @@
             {{ element.id }}
           </span>
         </div>
-        <p>{{ msg.text }}</p>
-
         <div v-if="msg.ref">
           <span class="small-tag blue" @click="searchRef(msg.ref)">
             reference
           </span>
         </div>
+        <p>{{ msg.text }}</p>
       </div>
     </div>
 
@@ -75,7 +74,7 @@ export default {
       api: {
         chatbot: "api/subgraph/chatbot",
       },
-      controller:null
+      controller: null,
     };
   },
   computed: {
@@ -115,21 +114,27 @@ export default {
     },
     searchInput(tag) {
       if (tag.type == "protein") {
-        this.$router.push(tag.mode);
-        this.emitter.emit("searchNode", { node: tag.data, mode: tag.mode });
+        this.$router.push(tag.mode).then(() => {
+          this.emitter.emit("searchNode", { node: tag.data, mode: tag.mode });
+        });
       } else if (tag.type == "term") {
         this.emitter.emit("searchEnrichment", tag.data);
       } else if (tag.type == "subset") {
-        this.$router.push(tag.mode);
-        this.emitter.emit("searchSubset", { subset: tag.data, mode: tag.mode });
+        this.$router.push(tag.mode).then(() => {
+          this.emitter.emit("searchSubset", {
+            subset: tag.data,
+            mode: tag.mode,
+          });
+        });
       }
     },
     searchRef(ref) {
       if (this.$store.state.citation_graph_data) {
-        this.$router.push("citation");
-        this.emitter.emit("searchSubset", {
-          subset: this.pmid_nodes(ref),
-          mode: "citation",
+        this.$router.push("citation").then(() => {
+          this.emitter.emit("searchfavouriteSubset", {
+            subset: this.pmid_nodes(ref),
+            mode: "citation",
+          });
         });
       } else {
         alert("no citation graph");
@@ -231,7 +236,7 @@ export default {
       // Create a new AbortController instance
       this.controller = new AbortController();
       const signal = this.controller.signal; // Get the signal
-  
+
       const botMessage = {
         sender: "Bot",
         text: "Waiting for response...", // Initially empty, will be updated progressively
@@ -268,9 +273,7 @@ export default {
           stream: !done,
         });
         // Parse the chunk as JSON to extract "messages" and "pmids"
-        console.log(chunk);
         let parsedChunk = JSON.parse(chunk);
-        console.log(parsedChunk);
         // Check if it's a message part or pmids
         if (parsedChunk.message) {
           // Append message chunks to the fullText

frontend/src/components/enrichment/PathwayList.vue

@@ -178,6 +178,7 @@ export default {
   watch: {
     terms() {
       this.filter_options(this.terms);
+      this.init_categories();
     },
   },
   computed: {
@@ -261,6 +262,18 @@ export default {
       this.category = "Filter";
       this.active_categories_set = new Set();
     },
+    init_categories() {
+      for (let element of this.filter_terms) {
+        let checkCategory = element.label;
+        if (
+          checkCategory !== "GOCC" &&
+          checkCategory !== "GOMF" &&
+          checkCategory !== "GOBP"
+        )
+          this.active_categories(checkCategory);
+      }
+      this.category = [...this.active_categories_set].join(", ");
+    },
     filter_options(terms) {
       var com = this;
       com.filter_terms = [];

frontend/src/components/enrichment/PathwaySet.vue

@@ -201,7 +201,7 @@ export default {
         id: `${subset.view}:${subset.name}`,
         mode: subset.view,
         type: "subset",
-        data: this.activate_genes(subset.genes),
+        data: this.activate_genes(subset.genes, subset.view),
       });
     },
     save_subset() {
@@ -240,25 +240,34 @@ export default {
         if (layer != entry) layer.status = false;
       }
 
-      this.$router.push(entry.view);
-      if (!entry.status) {
-        this.emitter.emit("searchSubset", {
-          subset: this.activate_genes(entry.genes),
-          mode: entry.view,
-        });
-        this.emitter.emit("enrichTerms", entry.terms);
-      } else {
-        this.emitter.emit("searchSubset", { subset: null, mode: entry.view });
-        this.emitter.emit("enrichTerms", null);
-      }
-      entry.status = !entry.status;
+      this.$router.push(entry.view).then(() => {
+        if (!entry.status) {
+          this.emitter.emit("searchSubset", {
+            subset: this.activate_genes(entry.genes, entry.view),
+            mode: entry.view,
+          });
+          this.emitter.emit("enrichTerms", entry.terms);
+        } else {
+          this.emitter.emit("searchSubset", { subset: null, mode: entry.view });
+          this.emitter.emit("enrichTerms", null);
+        }
+        entry.status = !entry.status;
+      });
     },
-    activate_genes(genes) {
-      var com = this;
+    activate_genes(genes, view) {
       var subset = [];
       var genes_set = new Set(genes);
+      let data;
+
+      if (view === "citation") {
+        data = this.$store.state.citation_graph_data.graph;
+      } else if (view === "term") {
+        data = this.$store.state.term_graph_data.graph;
+      } else if (view === "protein") {
+        data = this.$store.state.gephi_json.data;
+      }
 
-      com.gephi_data.nodes.forEach((node) => {
+      data.nodes.forEach((node) => {
         if (genes_set.has(node.attributes["Name"])) {
           subset.push(node);
         }

frontend/src/components/enrichment/PathwayTools.vue

@@ -195,6 +195,7 @@ export default {
 }
 
 .tool-buttons {
+  min-width: 2rem;
   padding: 0.2vw 0 0.2vw 0;
   border-radius: 0;
   cursor: pointer;

frontend/src/components/interface/NetworkValues.vue

@@ -19,12 +19,11 @@ export default {
 #network-values {
   width: 5%;
   height: 3.98%;
-  left: 25vw;
-  bottom: 1vw;
+  top: 1%;
   display: flex;
   flex-direction: column;
   justify-content: center;
-  position: absolute;
+  position: relative;
   /* border-radius: 5px; */
   -webkit-backdrop-filter: blur(7.5px);
   transition: left 0.5s ease-in-out;

frontend/src/components/pane/modules/node/NetworkStatistics.vue

@@ -115,6 +115,7 @@ export default {
 
 #statistics .network-results {
   overflow: scroll;
+  height: 100%;
 }
 
 .network-results::-webkit-scrollbar {

frontend/src/components/pane/modules/pathways/PathwayStatistics.vue

@@ -38,8 +38,8 @@ export default {
       if (com.active_term == null) {
         return;
       }
-      const { category, clean, fdr_rate, p_value } = com.active_term;
-      com.statistics = { category, clean, fdr_rate, p_value };
+      const { name, category, clean, fdr_rate, p_value } = com.active_term;
+      com.statistics = { name, category, clean, fdr_rate, p_value };
     },
   },
 };

frontend/src/components/toolbar/CitationToolBar.vue

@@ -81,7 +81,7 @@ export default {
       protein_active: false,
       selection_active: false,
       mode: "citation",
-      label_check: false,
+      label_check: true,
     };
   },
   methods: {

frontend/src/components/toolbar/MainToolBar.vue

@@ -89,7 +89,7 @@ export default {
       tools_active: false,
       protein_active: false,
       selection_active: false,
-      label_check: false,
+      label_check: true,
       mode: "protein",
     };
   },

frontend/src/components/toolbar/TermToolBar.vue

@@ -80,7 +80,7 @@ export default {
       tools_active: false,
       protein_active: false,
       selection_active: false,
-      label_check: false,
+      label_check: true,
       mode: "term",
     };
   },